Hey Matthew,
As a plot device why not use the X’lanthos in this manner.

1) The X’lanthos, an ancient race that long ago mastered Dark matter and created dark portal technology.

2) Over many centuries the X’lanthos expanded across the cosmos creating a thousand civilizations over thousands of worlds.

3) Each X’lanthos civilizations was distinct and diverse, some valued thought and study, others strength and stills others aggression and expansion.

4) So it was that an aggressive sect of X’lanthos found humanity.

5) In there haste to cleans yet another world the X’lanthos failed to see how much the human DNA resembled there own and the consequence that followed was that the very weapon used against humanity lead to the destruction of there own. In a single year a thousand X’lanthos civilizations on a thousand worlds vanished.

6) Now the survivors of the X’lanthos race fight to survive and rebuild, each pocket of peoples distinct and diverse from each other but with a common ancestry and technology base to draw from

Using this plot device would-

Allow X’lanthos Vs X’lanthos conflicts
Explain why and advance race would be at the same “level” as the other races/faction in the game.
Allow players to add there own flavor
Give a creation story and keep Dark portal creation as a lost technology

Me too. For whatever the reason, I like the idea that the X'lanthos have bloody schisms, fracturing them into a number of extremely dissimilar factions - and that this feeds into the exterminatory pursuit of the Changers by the X'lanthos faction in question (the Monoculture Collective).

I imagine that this isn't the first time that X'lanthos MC have been horribly sabotaged by Changers rebelling, like they totally crippled the XEF with their bioformer taint. Changer bioterrorists are incredibly dangerous.